Note

Go to the end to download the full example code

Using a validation set to monitor the convergence of the fugw loss#

In this example, we use 3 fMRI feature maps for training and 2 independant fMRI feature maps for testing to examine the evolutions of a training and a validation loss on 2 low-resolution brain volumes.

import numpy as np
import matplotlib.pyplot as plt

from nilearn import datasets, image, plotting
from scipy.spatial import distance_matrix
from fugw.mappings import FUGW

We first fetch 5 contrasts for each subject from the localizer dataset.

n_subjects = 2

contrasts = [
    "sentence reading vs checkerboard",
    "sentence listening",
    "calculation vs sentences",
    "left vs right button press",
    "checkerboard",
]
n_training_contrasts = 3

brain_data = datasets.fetch_localizer_contrasts(
    contrasts,
    n_subjects=n_subjects,
    get_anats=True,
    get_masks=True,
)

source_imgs_paths = brain_data["cmaps"][0 : len(contrasts)]
target_imgs_paths = brain_data["cmaps"][len(contrasts) : 2 * len(contrasts)]
source_mask = brain_data["masks"][0]

source_im = image.load_img(source_imgs_paths)
target_im = image.load_img(target_imgs_paths)
mask = image.load_img(source_mask)

/usr/local/lib/python3.8/site-packages/nilearn/datasets/func.py:893: UserWarning:

`legacy_format` will default to `False` in release 0.11. Dataset fetchers will then return pandas dataframes by default instead of recarrays.

We then downsample the images by 5 to reduce the computational cost.

SCALE_FACTOR = 5

resized_source_affine = source_im.affine.copy() * SCALE_FACTOR
resized_target_affine = target_im.affine.copy() * SCALE_FACTOR

source_im_resized = image.resample_img(source_im, resized_source_affine)
target_im_resized = image.resample_img(target_im, resized_target_affine)
mask_resized = image.resample_img(mask, resized_source_affine)

source_maps = np.nan_to_num(source_im_resized.get_fdata())
target_maps = np.nan_to_num(target_im_resized.get_fdata())
segmentation = mask_resized.get_fdata()

coordinates = np.argwhere(segmentation > 0)

source_features = source_maps[
    coordinates[:, 0], coordinates[:, 1], coordinates[:, 2]
].T
target_features = target_maps[
    coordinates[:, 0], coordinates[:, 1], coordinates[:, 2]
].T

fig = plt.figure()
ax = fig.add_subplot(projection="3d")
ax.scatter(coordinates[:, 0], coordinates[:, 1], coordinates[:, 2], marker="o")
ax.view_init(10, 135)
# make the panes transparent
ax.xaxis.set_pane_color((1.0, 1.0, 1.0, 0.0))
ax.yaxis.set_pane_color((1.0, 1.0, 1.0, 0.0))
ax.zaxis.set_pane_color((1.0, 1.0, 1.0, 0.0))
# make the grid lines transparent
ax.xaxis._axinfo["grid"]["color"] = (1, 1, 1, 0)
ax.yaxis._axinfo["grid"]["color"] = (1, 1, 1, 0)
ax.zaxis._axinfo["grid"]["color"] = (1, 1, 1, 0)
ax.set_title("3D voxel coordinates")
plt.show()
3D voxel coordinates
/usr/local/lib/python3.8/site-packages/nilearn/image/resampling.py:673: RuntimeWarning:

NaNs or infinite values are present in the data passed to resample. This is a bad thing as they make resampling ill-defined and much slower.

/usr/local/lib/python3.8/site-packages/nilearn/image/resampling.py:673: RuntimeWarning:

NaNs or infinite values are present in the data passed to resample. This is a bad thing as they make resampling ill-defined and much slower.

/usr/local/lib/python3.8/site-packages/nilearn/image/resampling.py:673: RuntimeWarning:

NaNs or infinite values are present in the data passed to resample. This is a bad thing as they make resampling ill-defined and much slower.

/usr/local/lib/python3.8/site-packages/nilearn/image/resampling.py:673: RuntimeWarning:

NaNs or infinite values are present in the data passed to resample. This is a bad thing as they make resampling ill-defined and much slower.

/usr/local/lib/python3.8/site-packages/nilearn/image/resampling.py:673: RuntimeWarning:

NaNs or infinite values are present in the data passed to resample. This is a bad thing as they make resampling ill-defined and much slower.

/usr/local/lib/python3.8/site-packages/nilearn/image/resampling.py:673: RuntimeWarning:

NaNs or infinite values are present in the data passed to resample. This is a bad thing as they make resampling ill-defined and much slower.

/usr/local/lib/python3.8/site-packages/nilearn/image/resampling.py:673: RuntimeWarning:

NaNs or infinite values are present in the data passed to resample. This is a bad thing as they make resampling ill-defined and much slower.

/usr/local/lib/python3.8/site-packages/nilearn/image/resampling.py:673: RuntimeWarning:

NaNs or infinite values are present in the data passed to resample. This is a bad thing as they make resampling ill-defined and much slower.

/usr/local/lib/python3.8/site-packages/nilearn/image/resampling.py:673: RuntimeWarning:

NaNs or infinite values are present in the data passed to resample. This is a bad thing as they make resampling ill-defined and much slower.

/usr/local/lib/python3.8/site-packages/nilearn/image/resampling.py:673: RuntimeWarning:

NaNs or infinite values are present in the data passed to resample. This is a bad thing as they make resampling ill-defined and much slower.

/usr/local/lib/python3.8/site-packages/nilearn/image/resampling.py:294: UserWarning:

Resampling binary images with continuous or linear interpolation. This might lead to unexpected results. You might consider using nearest interpolation instead.

We then compute the distance matrix between voxel coordinates.

source_geometry = distance_matrix(coordinates, coordinates)
target_geometry = source_geometry.copy()

In order to avoid numerical errors when fitting the mapping, we normalize both the features and the geometry.

source_features_normalized = source_features / np.linalg.norm(
    source_features, axis=1
).reshape(-1, 1)
target_features_normalized = target_features / np.linalg.norm(
    target_features, axis=1
).reshape(-1, 1)
source_geometry_normalized = source_geometry / np.max(source_geometry)
target_geometry_normalized = target_geometry / np.max(target_geometry)

We now fit the mapping using the sinkhorn solver and 10 BCD iterations. We use the first 3 feature maps for training and the last 2 for validation. Anatomical kernels are kept identical for both training and validation, as it will usually be the case in practice when aligning real fMRI data.

mapping = FUGW(alpha=0.5, rho=1, eps=1e-4)
_ = mapping.fit(
    source_features=source_features_normalized[:n_training_contrasts],
    target_features=target_features_normalized[:n_training_contrasts],
    source_geometry=source_geometry_normalized,
    target_geometry=target_geometry_normalized,
    source_features_val=source_features_normalized[n_training_contrasts:],
    target_features_val=target_features_normalized[n_training_contrasts:],
    solver="sinkhorn",
    solver_params={
        "nits_bcd": 10,
    },
    verbose=True,
)

[09:31:20] Validation data for anatomical kernels is not provided.  dense.py:220
           Using training data instead.


[09:31:33] BCD step 1/10   FUGW loss:      0.02656702883541584      dense.py:516
           Validation loss:        0.030553201213479042


[09:31:50] BCD step 2/10   FUGW loss:      0.012580208480358124     dense.py:516
           Validation loss:        0.01490649115294218


[09:32:07] BCD step 3/10   FUGW loss:      0.0102297468110919       dense.py:516
           Validation loss:        0.011878890916705132


[09:32:24] BCD step 4/10   FUGW loss:      0.00984442513436079      dense.py:516
           Validation loss:        0.011247879825532436


[09:32:40] BCD step 5/10   FUGW loss:      0.009588735178112984     dense.py:516
           Validation loss:        0.010830309242010117


[09:32:57] BCD step 6/10   FUGW loss:      0.009423702955245972     dense.py:516
           Validation loss:        0.010599419474601746


[09:33:13] BCD step 7/10   FUGW loss:      0.00930894073098898      dense.py:516
           Validation loss:        0.010493207722902298


[09:33:29] BCD step 8/10   FUGW loss:      0.00920107588171959      dense.py:516
           Validation loss:        0.010404211468994617


[09:33:46] BCD step 9/10   FUGW loss:      0.009097806178033352     dense.py:516
           Validation loss:        0.010211914777755737


[09:34:02] BCD step 10/10  FUGW loss:      0.00905172061175108      dense.py:516
           Validation loss:        0.010106153786182404

Plot the evolution of losses on train and test datasets.

fig, ax1 = plt.subplots()
ax1.set_xlabel("BCD Step")
ax1.set_ylabel("FUGW loss", color="black")
ax1.tick_params(axis="y", labelcolor="black")

ax1.plot(mapping.loss_steps, mapping.loss["total"], color="blue")
ax1.plot(mapping.loss_steps, mapping.loss_val["total"], color="red")

plt.title("Training and validation losses")
plt.legend(["Train", "Validation"])
fig.tight_layout()  # otherwise the right y-label is slightly clipped
plt.show()
Training and validation losses

Plot the alignment of the second validation feature map and project it on the fsaverage5 surface.

example_array = np.nan_to_num(source_im_resized.slicer[..., -1].get_fdata())
example_array /= np.max(np.abs(example_array))
example = image.new_img_like(source_im_resized, example_array)
plotting.view_img_on_surf(example, threshold="50%", surf_mesh="fsaverage5")


Total running time of the script: ( 2 minutes 44.325 seconds)

Estimated memory usage: 8 MB

Gallery generated by Sphinx-Gallery